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class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1 data-toc-skip>Changelog <small></small></h1> + + </div> +</nav><div class="container template-news"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Changelog</h1> <small>Source: <a href="https://github.com/jranke/mkin/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.6" id="mkin-126">mkin 1.2.6<a class="anchor" aria-label="anchor" href="#mkin-126"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.6" id="mkin-126">mkin 1.2.6<a class="anchor" aria-label="anchor" href="#mkin-126"></a></h2> <ul><li>‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Fix an erroneous call to the ‘endpoints()’ function</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.5" id="mkin-125-2023-08-09">mkin 1.2.5 (2023-08-09)<a class="anchor" aria-label="anchor" href="#mkin-125-2023-08-09"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.5" id="mkin-125-2023-08-09">mkin 1.2.5 (2023-08-09)<a class="anchor" aria-label="anchor" href="#mkin-125-2023-08-09"></a></h2> <ul><li><p>‘vignettes/mesotrione_parent_2023.rnw’: Prebuilt vignette showing how covariate modelling can be done for all relevant parent degradation models.</p></li> <li><p>‘inst/testdata/mesotrione_soil_efsa_2016}.xlsx’: Another example spreadsheets for use with ‘read_spreadsheet()’, featuring pH dependent degradation</p></li> <li><p>R/illparms.R: Fix the detection of ill-defined slope or error model parameters for the case that the estimate is negative</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.4" id="mkin-124-2023-05-19">mkin 1.2.4 (2023-05-19)<a class="anchor" aria-label="anchor" href="#mkin-124-2023-05-19"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.4" id="mkin-124-2023-05-19">mkin 1.2.4 (2023-05-19)<a class="anchor" aria-label="anchor" href="#mkin-124-2023-05-19"></a></h2> <ul><li>R/endpoints.R: Fix the calculation of endpoints for user specified covariate values</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.3.1" id="mkin-1231-unreleased">mkin 1.2.3.1 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-1231-unreleased"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.3.1" id="mkin-1231-unreleased">mkin 1.2.3.1 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-1231-unreleased"></a></h2> <ul><li>Small fixes to get the online docs right (example code in R/hierarchical_kinetics, cluster setup in cyantraniliprole and dmta pathway vignettes, graphics and model comparison in multistart vignette), rebuild online docs</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.3" id="mkin-123-2023-04-17">mkin 1.2.3 (2023-04-17)<a class="anchor" aria-label="anchor" href="#mkin-123-2023-04-17"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.3" id="mkin-123-2023-04-17">mkin 1.2.3 (2023-04-17)<a class="anchor" aria-label="anchor" href="#mkin-123-2023-04-17"></a></h2> <ul><li><p>‘R/{endpoints,parms,plot.mixed.mmkin,summary.saem.mmkin}.R’: Calculate parameters and endpoints and plot population curves for specific covariate values, or specific percentiles of covariate values used in saem fits.</p></li> <li><p>Depend on current deSolve version with the possibility to avoid resolving symbols in a shared library (compiled models) over and over, thanks to Thomas Petzoldt.</p></li> <li><p>‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Start a new cluster after creating a model stored in the user specified location, because otherwise symbols are not found by the worker processes.</p></li> @@ -134,7 +99,7 @@ <li><p>‘R/mkinerrmin.R’: Fix typo in subset (use of = instead of ==), thanks to Sebastian Meyer for spotting this during his work on R 4.3.0.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.2" id="mkin-122-unreleased">mkin 1.2.2 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-122-unreleased"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.2" id="mkin-122-unreleased">mkin 1.2.2 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-122-unreleased"></a></h2> <ul><li><p>‘inst/rmarkdown/templates/hierarchical_kinetics’: R markdown template to facilitate the application of hierarchical kinetic models.</p></li> <li><p>‘inst/testdata/{cyantraniliprole_soil_efsa_2014,lambda-cyhalothrin_soil_efsa_2014}.xlsx’: Example spreadsheets for use with ‘read_spreadsheet()’.</p></li> <li><p>‘R/mhmkin.R’: Allow an ‘illparms.mhmkin’ object or a list with suitable dimensions as value of the argument ‘no_random_effects’, making it possible to exclude random effects that were ill-defined in simpler variants of the set of degradation models. Remove the possibility to exclude random effects based on separate fits, as it did not work well.</p></li> @@ -145,7 +110,7 @@ <li><p>‘R/intervals.R’: Include correlations of random effects in the model in case there are any.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.1" id="mkin-121-2022-11-19">mkin 1.2.1 (2022-11-19)<a class="anchor" aria-label="anchor" href="#mkin-121-2022-11-19"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.1" id="mkin-121-2022-11-19">mkin 1.2.1 (2022-11-19)<a class="anchor" aria-label="anchor" href="#mkin-121-2022-11-19"></a></h2> <ul><li><p>‘{data,R}/ds_mixed.rda’: Include the test data in the package instead of generating it in ‘tests/testthat/setup_script.R’. Refactor the generating code to make it consistent and update tests.</p></li> <li><p>‘tests/testthat/setup_script.R’: Excluded another ill-defined random effect for the DFOP fit with ‘saem’, in an attempt to avoid a platform dependence that surfaced on Fedora systems on the CRAN check farm</p></li> <li><p>‘tests/testthat/test_mixed.R’: Round parameters found by saemix to two significant digits before printing, to also help to avoid platform dependence of tests</p></li> @@ -154,7 +119,7 @@ <li><p>‘R/loglik.mkinfit.R’: Add ‘nobs’ attribute to the resulting ‘logLik’ object, in order to make test_AIC.R succeed on current R-devel</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-2022-11-17">mkin 1.2.0 (2022-11-17)<a class="anchor" aria-label="anchor" href="#mkin-120-2022-11-17"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.0" id="mkin-120-2022-11-17">mkin 1.2.0 (2022-11-17)<a class="anchor" aria-label="anchor" href="#mkin-120-2022-11-17"></a></h2> <ul><li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li> <li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li> <li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li> @@ -168,7 +133,7 @@ <li><p>‘R/tex_listings.R’: Conveniently include summaries of fit objects in R markdown documents that are compiled to LaTeX.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.1.1" id="mkin-111-2022-07-12">mkin 1.1.1 (2022-07-12)<a class="anchor" aria-label="anchor" href="#mkin-111-2022-07-12"></a></h2> +<h2 class="pkg-version" data-toc-text="1.1.1" id="mkin-111-2022-07-12">mkin 1.1.1 (2022-07-12)<a class="anchor" aria-label="anchor" href="#mkin-111-2022-07-12"></a></h2> <ul><li><p>’R/{mkinmod,mkinpredict}.R: Store DLL information in mkinmod objects and use that information in mkinpredict to avoid a performance regression brought by a bugfix in R 4.2.x. Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel list and his suggestion on how to fix it.</p></li> <li><p>‘vignettes/FOCUS_L.rmd’: Remove an outdated note referring to a failure to calculate the covariance matrix for DFOP with the L2 dataset. Since 0.9.45.5 the covariance matrix is available</p></li> <li><p>‘vignettes/web_only/benchmarks.rmd’: Add the first benchmark data using my laptop system, therefore add the CPU when showing the benchmark results.</p></li> @@ -180,7 +145,7 @@ <li><p>‘plot.mkinfit’: Respect argument ‘maxabs’ for residual plots, and make it possible to give ylim as a list, for row layouts</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.1.0" id="mkin-110-2022-03-14">mkin 1.1.0 (2022-03-14)<a class="anchor" aria-label="anchor" href="#mkin-110-2022-03-14"></a></h2> +<h2 class="pkg-version" data-toc-text="1.1.0" id="mkin-110-2022-03-14">mkin 1.1.0 (2022-03-14)<a class="anchor" aria-label="anchor" href="#mkin-110-2022-03-14"></a></h2> <div class="section level3"> <h3 id="mixed-effects-models-1-1-0">Mixed-effects models<a class="anchor" aria-label="anchor" href="#mixed-effects-models-1-1-0"></a></h3> <ul><li><p>Reintroduce the interface to saemix version 3.0 (now on CRAN), in particular the generic function ‘saem’ with a generator ‘saem.mmkin’, currently using ‘saemix_model’ and ‘saemix_data’, summary and plot methods</p></li> @@ -191,25 +156,25 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.5" id="mkin-105-2021-09-15">mkin 1.0.5 (2021-09-15)<a class="anchor" aria-label="anchor" href="#mkin-105-2021-09-15"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.5" id="mkin-105-2021-09-15">mkin 1.0.5 (2021-09-15)<a class="anchor" aria-label="anchor" href="#mkin-105-2021-09-15"></a></h2> <ul><li>‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.4" id="mkin-104-2021-04-20">mkin 1.0.4 (2021-04-20)<a class="anchor" aria-label="anchor" href="#mkin-104-2021-04-20"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.4" id="mkin-104-2021-04-20">mkin 1.0.4 (2021-04-20)<a class="anchor" aria-label="anchor" href="#mkin-104-2021-04-20"></a></h2> <ul><li><p>All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters</p></li> <li><p>‘plot.mkinfit’: Use xlab and xlim for the residual plot if show_residuals is TRUE</p></li> <li><p>‘mmkin’: Use cores = 1 per default on Windows to make it easier for first time users</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.3" id="mkin-103-2021-02-15">mkin 1.0.3 (2021-02-15)<a class="anchor" aria-label="anchor" href="#mkin-103-2021-02-15"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.3" id="mkin-103-2021-02-15">mkin 1.0.3 (2021-02-15)<a class="anchor" aria-label="anchor" href="#mkin-103-2021-02-15"></a></h2> <ul><li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.2" id="mkin-102-unreleased">mkin 1.0.2 (Unreleased)<a class="anchor" aria-label="anchor" href="#mkin-102-unreleased"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.2" id="mkin-102-unreleased">mkin 1.0.2 (Unreleased)<a class="anchor" aria-label="anchor" href="#mkin-102-unreleased"></a></h2> <ul><li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.1" id="mkin-101-2021-02-10">mkin 1.0.1 (2021-02-10)<a class="anchor" aria-label="anchor" href="#mkin-101-2021-02-10"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.1" id="mkin-101-2021-02-10">mkin 1.0.1 (2021-02-10)<a class="anchor" aria-label="anchor" href="#mkin-101-2021-02-10"></a></h2> <ul><li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li> <li><p>‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax</p></li> <li><p>‘mkinresplot’: Re-add Katrin Lindenberger as coauthor who was accidentally removed long ago</p></li> @@ -217,7 +182,7 @@ <li><p>Increase test tolerance for some parameter comparisons that also proved to be platform dependent</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.0" id="mkin-100-2021-02-03">mkin 1.0.0 (2021-02-03)<a class="anchor" aria-label="anchor" href="#mkin-100-2021-02-03"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.0" id="mkin-100-2021-02-03">mkin 1.0.0 (2021-02-03)<a class="anchor" aria-label="anchor" href="#mkin-100-2021-02-03"></a></h2> <div class="section level3"> <h3 id="general-1-0-0">General<a class="anchor" aria-label="anchor" href="#general-1-0-0"></a></h3> <ul><li><p>‘mkinmod’ models gain arguments ‘name’ and ‘dll_dir’ which, in conjunction with a current version of the ‘inline’ package, make it possible to still use the DLL used for fast ODE solutions with ‘deSolve’ after saving and restoring the ‘mkinmod’ object.</p></li> @@ -238,7 +203,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.50.3" id="mkin-09503-2020-10-08">mkin 0.9.50.3 (2020-10-08)<a class="anchor" aria-label="anchor" href="#mkin-09503-2020-10-08"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.50.3" id="mkin-09503-2020-10-08">mkin 0.9.50.3 (2020-10-08)<a class="anchor" aria-label="anchor" href="#mkin-09503-2020-10-08"></a></h2> <ul><li><p>‘parms’: Add a method for mmkin objects</p></li> <li><p>‘mmkin’ and ‘confint(method = ’profile’): Use all cores detected by parallel::detectCores() per default</p></li> <li><p>‘confint(method = ’profile’): Choose accuracy based on ‘rel_tol’ argument, relative to the bounds obtained by the quadratic approximation</p></li> @@ -250,22 +215,22 @@ <li><p>‘endpoints’: Back-calculate DT50 value from DT90 also for the biphasic models DFOP, HS and SFORB</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.50.2" id="mkin-09502-2020-05-12">mkin 0.9.50.2 (2020-05-12)<a class="anchor" aria-label="anchor" href="#mkin-09502-2020-05-12"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.50.2" id="mkin-09502-2020-05-12">mkin 0.9.50.2 (2020-05-12)<a class="anchor" aria-label="anchor" href="#mkin-09502-2020-05-12"></a></h2> <ul><li><p>Increase tolerance for a platform specific test results on the Solaris test machine on CRAN</p></li> <li><p>Updates and corrections (using the spelling package) to the documentation</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.50.1" id="mkin-09501-2020-05-11">mkin 0.9.50.1 (2020-05-11)<a class="anchor" aria-label="anchor" href="#mkin-09501-2020-05-11"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.50.1" id="mkin-09501-2020-05-11">mkin 0.9.50.1 (2020-05-11)<a class="anchor" aria-label="anchor" href="#mkin-09501-2020-05-11"></a></h2> <ul><li><p>Support SFORB with formation fractions</p></li> <li><p>‘mkinmod’: Make ‘use_of_ff’ = “max” the default</p></li> <li><p>Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.11" id="mkin-094911-2020-04-20">mkin 0.9.49.11 (2020-04-20)<a class="anchor" aria-label="anchor" href="#mkin-094911-2020-04-20"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.11" id="mkin-094911-2020-04-20">mkin 0.9.49.11 (2020-04-20)<a class="anchor" aria-label="anchor" href="#mkin-094911-2020-04-20"></a></h2> <ul><li>Increase a test tolerance to make it pass on all CRAN check machines</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.10" id="mkin-094910-2020-04-18">mkin 0.9.49.10 (2020-04-18)<a class="anchor" aria-label="anchor" href="#mkin-094910-2020-04-18"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.10" id="mkin-094910-2020-04-18">mkin 0.9.49.10 (2020-04-18)<a class="anchor" aria-label="anchor" href="#mkin-094910-2020-04-18"></a></h2> <ul><li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods</p></li> <li><p>‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects</p></li> <li><p>‘endpoints’: Don’t return the SFORB list component if it’s empty. This reduces distraction and complies with the documentation</p></li> @@ -274,12 +239,12 @@ <li><p>‘summary.mkinfit’: Add AIC, BIC and log likelihood to the summary</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.9" id="mkin-09499-2020-03-31">mkin 0.9.49.9 (2020-03-31)<a class="anchor" aria-label="anchor" href="#mkin-09499-2020-03-31"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.9" id="mkin-09499-2020-03-31">mkin 0.9.49.9 (2020-03-31)<a class="anchor" aria-label="anchor" href="#mkin-09499-2020-03-31"></a></h2> <ul><li><p>‘mkinmod’: Use pkgbuild::has_compiler instead of Sys.which(‘gcc’), as the latter will often fail even if Rtools are installed</p></li> <li><p>‘mkinds’: Use roxygen for documenting fields and methods of this R6 class</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.8" id="mkin-09498-2020-01-09">mkin 0.9.49.8 (2020-01-09)<a class="anchor" aria-label="anchor" href="#mkin-09498-2020-01-09"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.8" id="mkin-09498-2020-01-09">mkin 0.9.49.8 (2020-01-09)<a class="anchor" aria-label="anchor" href="#mkin-09498-2020-01-09"></a></h2> <ul><li><p>‘aw’: Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns</p></li> <li><p>‘loftest’: Add a lack-of-fit test</p></li> <li><p>‘plot_res’, ‘plot_sep’ and ‘mkinerrplot’: Add the possibility to show standardized residuals and make it the default for fits with error models other than ‘const’</p></li> @@ -287,12 +252,12 @@ <li><p>‘confint.mkinfit’: Make the quadratic approximation the default, as the likelihood profiling takes a lot of time, especially if the fit has more than three parameters</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.7" id="mkin-09497-2019-11-01">mkin 0.9.49.7 (2019-11-01)<a class="anchor" aria-label="anchor" href="#mkin-09497-2019-11-01"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.7" id="mkin-09497-2019-11-01">mkin 0.9.49.7 (2019-11-01)<a class="anchor" aria-label="anchor" href="#mkin-09497-2019-11-01"></a></h2> <ul><li><p>Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation</p></li> <li><p>Add a ‘nobs’ method for mkinfit objects, enabling the default ‘BIC’ method from the stats package. Also, add a ‘BIC’ method for mmkin column objects.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.6" id="mkin-09496-2019-10-31">mkin 0.9.49.6 (2019-10-31)<a class="anchor" aria-label="anchor" href="#mkin-09496-2019-10-31"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.6" id="mkin-09496-2019-10-31">mkin 0.9.49.6 (2019-10-31)<a class="anchor" aria-label="anchor" href="#mkin-09496-2019-10-31"></a></h2> <ul><li><p>Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package</p></li> <li><p>Add an ‘update’ method for mkinfit objects which remembers fitted parameters if appropriate</p></li> <li><p>Add a ‘residuals’ method for mkinfit objects that supports scaling based on the error model</p></li> @@ -308,7 +273,7 @@ <li><p>Support summarizing ‘mkinfit’ objects generated with versions < 0.9.49.5</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.5" id="mkin-09495-2019-07-04">mkin 0.9.49.5 (2019-07-04)<a class="anchor" aria-label="anchor" href="#mkin-09495-2019-07-04"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.5" id="mkin-09495-2019-07-04">mkin 0.9.49.5 (2019-07-04)<a class="anchor" aria-label="anchor" href="#mkin-09495-2019-07-04"></a></h2> <ul><li><p>Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm ‘d_3’ tries direct minimization and a three-step procedure, and returns the model with the highest likelihood.</p></li> <li><p>The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ and ‘error_model_algorithm’ instead</p></li> <li><p>Add a test that checks if we get the best known AIC for parent only fits to 12 test datasets. Add these test datasets for this purpose.</p></li> @@ -323,7 +288,7 @@ <li><p>Add example datasets obtained from risk assessment reports published by the European Food Safety Agency.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.48.1" id="mkin-09481-2019-03-04">mkin 0.9.48.1 (2019-03-04)<a class="anchor" aria-label="anchor" href="#mkin-09481-2019-03-04"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.48.1" id="mkin-09481-2019-03-04">mkin 0.9.48.1 (2019-03-04)<a class="anchor" aria-label="anchor" href="#mkin-09481-2019-03-04"></a></h2> <ul><li><p>Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects</p></li> <li><p>Add the function ‘AIC.mmkin’ to make it easy to compare columns of mmkin objects</p></li> <li><p>‘add_err’: Respect the argument giving the number of replicates in the synthetic dataset</p></li> @@ -336,23 +301,23 @@ <li><p>‘nafta’: Add evaluations according to the NAFTA guidance</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.47.5" id="mkin-09475-2018-09-14">mkin 0.9.47.5 (2018-09-14)<a class="anchor" aria-label="anchor" href="#mkin-09475-2018-09-14"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.47.5" id="mkin-09475-2018-09-14">mkin 0.9.47.5 (2018-09-14)<a class="anchor" aria-label="anchor" href="#mkin-09475-2018-09-14"></a></h2> <ul><li><p>Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows</p></li> <li><p>Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)</p></li> <li><p>Exclude more example code from testing on CRAN to avoid NOTES from long execution times</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.47.3" id="mkin-09473">mkin 0.9.47.3<a class="anchor" aria-label="anchor" href="#mkin-09473"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.47.3" id="mkin-09473">mkin 0.9.47.3<a class="anchor" aria-label="anchor" href="#mkin-09473"></a></h2> <ul><li><p>‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’</p></li> <li><p>Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.47.2" id="mkin-09472-2018-07-19">mkin 0.9.47.2 (2018-07-19)<a class="anchor" aria-label="anchor" href="#mkin-09472-2018-07-19"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.47.2" id="mkin-09472-2018-07-19">mkin 0.9.47.2 (2018-07-19)<a class="anchor" aria-label="anchor" href="#mkin-09472-2018-07-19"></a></h2> <ul><li><p>‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.</p></li> <li><p>‘mkinfit’: Use 1.1 as starting value for N parameter of IORE models to obtain convergence in more difficult cases. Show parameter names when ‘trace_parms’ is ‘TRUE’.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.47.1" id="mkin-09471-2018-02-06">mkin 0.9.47.1 (2018-02-06)<a class="anchor" aria-label="anchor" href="#mkin-09471-2018-02-06"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.47.1" id="mkin-09471-2018-02-06">mkin 0.9.47.1 (2018-02-06)<a class="anchor" aria-label="anchor" href="#mkin-09471-2018-02-06"></a></h2> <ul><li><p>Skip some tests on CRAN and winbuilder to avoid timeouts</p></li> <li><p>‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014</p></li> <li><p>‘mkinfit’: Added the iterative reweighting method ‘tc’ using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more.</p></li> @@ -361,41 +326,41 @@ <li><p>‘summary.mkinfit’: Show versions of mkin and R used for fitting (not the ones used for the summary) if the fit was generated with mkin >= 0.9.47.1</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.46.3" id="mkin-09463-2017-11-16">mkin 0.9.46.3 (2017-11-16)<a class="anchor" aria-label="anchor" href="#mkin-09463-2017-11-16"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.46.3" id="mkin-09463-2017-11-16">mkin 0.9.46.3 (2017-11-16)<a class="anchor" aria-label="anchor" href="#mkin-09463-2017-11-16"></a></h2> <ul><li><p><code>README.md</code>, <code>vignettes/mkin.Rmd</code>: URLs were updated</p></li> <li><p><code>synthetic_data_for_UBA</code>: Add the code used to generate the data in the interest of reproducibility</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.46.2" id="mkin-09462-2017-10-10">mkin 0.9.46.2 (2017-10-10)<a class="anchor" aria-label="anchor" href="#mkin-09462-2017-10-10"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.46.2" id="mkin-09462-2017-10-10">mkin 0.9.46.2 (2017-10-10)<a class="anchor" aria-label="anchor" href="#mkin-09462-2017-10-10"></a></h2> <ul><li><p>Converted the vignette FOCUS_Z from tex/pdf to markdown/html</p></li> <li><p><code>DESCRIPTION</code>: Add ORCID</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.46.1" id="mkin-09461-2017-09-14">mkin 0.9.46.1 (2017-09-14)<a class="anchor" aria-label="anchor" href="#mkin-09461-2017-09-14"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.46.1" id="mkin-09461-2017-09-14">mkin 0.9.46.1 (2017-09-14)<a class="anchor" aria-label="anchor" href="#mkin-09461-2017-09-14"></a></h2> <ul><li><p><code>plot.mkinfit</code>: Fix scaling of residual plots for the case of separate plots for each observed variable</p></li> <li><p><code>plot.mkinfit</code>: Use all data points of the fitted curve for y axis scaling for the case of separate plots for each observed variable</p></li> <li><p>Documentation updates</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.46" id="mkin-0946-2017-07-24">mkin 0.9.46 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-0946-2017-07-24"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.46" id="mkin-0946-2017-07-24">mkin 0.9.46 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-0946-2017-07-24"></a></h2> <ul><li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.45.2" id="mkin-09452-2017-07-24">mkin 0.9.45.2 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09452-2017-07-24"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.45.2" id="mkin-09452-2017-07-24">mkin 0.9.45.2 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09452-2017-07-24"></a></h2> <ul><li><p>Rename <code>twa</code> to <code>max_twa_parent</code> to avoid conflict with <code>twa</code> from my <code>pfm</code> package</p></li> <li><p>Update URLs in documentation</p></li> <li><p>Limit test code to one core to pass on windows</p></li> <li><p>Switch from <code>microbenchmark</code> to <code>rbenchmark</code> as the former is not supported on all platforms</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.45.1" id="mkin-09451-2016-12-20">mkin 0.9.45.1 (2016-12-20)<a class="anchor" aria-label="anchor" href="#mkin-09451-2016-12-20"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.45.1" id="mkin-09451-2016-12-20">mkin 0.9.45.1 (2016-12-20)<a class="anchor" aria-label="anchor" href="#mkin-09451-2016-12-20"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-45-1">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-45-1"></a></h3> <ul><li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li> </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.45" id="mkin-0945-2016-12-08">mkin 0.9.45 (2016-12-08)<a class="anchor" aria-label="anchor" href="#mkin-0945-2016-12-08"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.45" id="mkin-0945-2016-12-08">mkin 0.9.45 (2016-12-08)<a class="anchor" aria-label="anchor" href="#mkin-0945-2016-12-08"></a></h2> <div class="section level3"> <h3 id="minor-changes-0-9-45">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-45"></a></h3> <ul><li><p><code>plot.mkinfit</code> and <code>plot.mmkin</code>: If the plotting device is <code>tikz</code>, LaTeX markup is being used for the chi2 error in the graphs.</p></li> @@ -404,14 +369,14 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.44" id="mkin-0944-2016-06-29">mkin 0.9.44 (2016-06-29)<a class="anchor" aria-label="anchor" href="#mkin-0944-2016-06-29"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.44" id="mkin-0944-2016-06-29">mkin 0.9.44 (2016-06-29)<a class="anchor" aria-label="anchor" href="#mkin-0944-2016-06-29"></a></h2> <div class="section level3"> <h3 id="bug-fixes-0-9-44">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-44"></a></h3> <ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li> </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.43" id="mkin-0943-2016-06-28">mkin 0.9.43 (2016-06-28)<a class="anchor" aria-label="anchor" href="#mkin-0943-2016-06-28"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.43" id="mkin-0943-2016-06-28">mkin 0.9.43 (2016-06-28)<a class="anchor" aria-label="anchor" href="#mkin-0943-2016-06-28"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-43">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-43"></a></h3> <ul><li><p>The title was changed to <code>Kinetic evaluations of chemical degradation data</code></p></li> @@ -439,7 +404,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.42" id="mkin-0942-2016-03-25">mkin 0.9.42 (2016-03-25)<a class="anchor" aria-label="anchor" href="#mkin-0942-2016-03-25"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.42" id="mkin-0942-2016-03-25">mkin 0.9.42 (2016-03-25)<a class="anchor" aria-label="anchor" href="#mkin-0942-2016-03-25"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-42">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-42"></a></h3> <ul><li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li> @@ -452,7 +417,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-41" id="mkin-09-41-2015-11-09">mkin 0.9-41 (2015-11-09)<a class="anchor" aria-label="anchor" href="#mkin-09-41-2015-11-09"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-41" id="mkin-09-41-2015-11-09">mkin 0.9-41 (2015-11-09)<a class="anchor" aria-label="anchor" href="#mkin-09-41-2015-11-09"></a></h2> <div class="section level3"> <h3 id="minor-changes-0-9-41">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-41"></a></h3> <ul><li><p>Add an R6 class <code>mkinds</code> representing datasets with a printing method</p></li> @@ -467,7 +432,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-40" id="mkin-09-40-2015-07-21">mkin 0.9-40 (2015-07-21)<a class="anchor" aria-label="anchor" href="#mkin-09-40-2015-07-21"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-40" id="mkin-09-40-2015-07-21">mkin 0.9-40 (2015-07-21)<a class="anchor" aria-label="anchor" href="#mkin-09-40-2015-07-21"></a></h2> <div class="section level3"> <h3 id="bug-fixes-0-9-40">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-40"></a></h3> <ul><li> @@ -480,7 +445,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-39" id="mkin-09-39-2015-06-26">mkin 0.9-39 (2015-06-26)<a class="anchor" aria-label="anchor" href="#mkin-09-39-2015-06-26"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-39" id="mkin-09-39-2015-06-26">mkin 0.9-39 (2015-06-26)<a class="anchor" aria-label="anchor" href="#mkin-09-39-2015-06-26"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-39">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-39"></a></h3> <ul><li><p>New function <code><a href="../reference/mmkin.html">mmkin()</a></code>: This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. A subsetting method with single brackets is available. Fitting the models in parallel using the <code>parallel</code> package is supported.</p></li> @@ -493,7 +458,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-38" id="mkin-09-38-2015-06-24">mkin 0.9-38 (2015-06-24)<a class="anchor" aria-label="anchor" href="#mkin-09-38-2015-06-24"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-38" id="mkin-09-38-2015-06-24">mkin 0.9-38 (2015-06-24)<a class="anchor" aria-label="anchor" href="#mkin-09-38-2015-06-24"></a></h2> <div class="section level3"> <h3 id="minor-changes-0-9-38">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-38"></a></h3> <ul><li><p><code>vignettes/compiled_models.html</code>: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.</p></li> @@ -506,7 +471,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-36" id="mkin-09-36-2015-06-21">mkin 0.9-36 (2015-06-21)<a class="anchor" aria-label="anchor" href="#mkin-09-36-2015-06-21"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-36" id="mkin-09-36-2015-06-21">mkin 0.9-36 (2015-06-21)<a class="anchor" aria-label="anchor" href="#mkin-09-36-2015-06-21"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-36">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-36"></a></h3> <ul><li><p><code><a href="../reference/summary.mkinfit.html">summary.mkinfit()</a></code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> @@ -520,7 +485,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-35" id="mkin-09-35-2015-05-15">mkin 0.9-35 (2015-05-15)<a class="anchor" aria-label="anchor" href="#mkin-09-35-2015-05-15"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-35" id="mkin-09-35-2015-05-15">mkin 0.9-35 (2015-05-15)<a class="anchor" aria-label="anchor" href="#mkin-09-35-2015-05-15"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-35">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-35"></a></h3> <ul><li>Switch from RUnit to testthat for testing</li> @@ -541,7 +506,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-34" id="mkin-09-34-2014-11-22">mkin 0.9-34 (2014-11-22)<a class="anchor" aria-label="anchor" href="#mkin-09-34-2014-11-22"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-34" id="mkin-09-34-2014-11-22">mkin 0.9-34 (2014-11-22)<a class="anchor" aria-label="anchor" href="#mkin-09-34-2014-11-22"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-34">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-34"></a></h3> <ul><li><p>Add the convenience function <code><a href="../reference/mkinmod.html">mkinsub()</a></code> for creating the lists used in <code><a href="../reference/mkinmod.html">mkinmod()</a></code></p></li> @@ -555,7 +520,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-33" id="mkin-09-33-2014-10-22">mkin 0.9-33 (2014-10-22)<a class="anchor" aria-label="anchor" href="#mkin-09-33-2014-10-22"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-33" id="mkin-09-33-2014-10-22">mkin 0.9-33 (2014-10-22)<a class="anchor" aria-label="anchor" href="#mkin-09-33-2014-10-22"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-33">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-33"></a></h3> <ul><li><p>The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and <code>state.ini = "auto"</code></p></li> @@ -577,7 +542,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-32" id="mkin-09-32-2014-07-24">mkin 0.9-32 (2014-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09-32-2014-07-24"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-32" id="mkin-09-32-2014-07-24">mkin 0.9-32 (2014-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09-32-2014-07-24"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-32">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-32"></a></h3> <ul><li><p>The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.</p></li> @@ -603,14 +568,14 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-31" id="mkin-09-31-2014-07-14">mkin 0.9-31 (2014-07-14)<a class="anchor" aria-label="anchor" href="#mkin-09-31-2014-07-14"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-31" id="mkin-09-31-2014-07-14">mkin 0.9-31 (2014-07-14)<a class="anchor" aria-label="anchor" href="#mkin-09-31-2014-07-14"></a></h2> <div class="section level3"> <h3 id="bug-fixes-0-9-31">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-31"></a></h3> <ul><li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li> </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-30" id="mkin-09-30-2014-07-11">mkin 0.9-30 (2014-07-11)<a class="anchor" aria-label="anchor" href="#mkin-09-30-2014-07-11"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-30" id="mkin-09-30-2014-07-11">mkin 0.9-30 (2014-07-11)<a class="anchor" aria-label="anchor" href="#mkin-09-30-2014-07-11"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-30">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-30"></a></h3> <ul><li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li> @@ -631,19 +596,19 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-29" id="mkin-09-29-2014-06-27">mkin 0.9-29 (2014-06-27)<a class="anchor" aria-label="anchor" href="#mkin-09-29-2014-06-27"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-29" id="mkin-09-29-2014-06-27">mkin 0.9-29 (2014-06-27)<a class="anchor" aria-label="anchor" href="#mkin-09-29-2014-06-27"></a></h2> <ul><li><p>R/mkinresplot.R: Make it possible to specify <code>xlim</code></p></li> <li><p>R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function</p></li> <li><p>R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-28" id="mkin-09-28-2014-05-20">mkin 0.9-28 (2014-05-20)<a class="anchor" aria-label="anchor" href="#mkin-09-28-2014-05-20"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-28" id="mkin-09-28-2014-05-20">mkin 0.9-28 (2014-05-20)<a class="anchor" aria-label="anchor" href="#mkin-09-28-2014-05-20"></a></h2> <ul><li><p>Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set</p></li> <li><p>Add historical remarks and some background to the main package vignette</p></li> <li><p>Correct ‘isotropic’ into ‘isometric’ for the ilr transformation</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-27" id="mkin-09-27-2014-05-10">mkin 0.9-27 (2014-05-10)<a class="anchor" aria-label="anchor" href="#mkin-09-27-2014-05-10"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-27" id="mkin-09-27-2014-05-10">mkin 0.9-27 (2014-05-10)<a class="anchor" aria-label="anchor" href="#mkin-09-27-2014-05-10"></a></h2> <ul><li><p>Fork the GUI into a separate package <a href="https://github.com/jranke/gmkin" class="external-link">gmkin</a></p></li> <li><p>DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information</p></li> <li><p>Remove files belonging to the GUI</p></li> @@ -663,13 +628,13 @@ <li><p>Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-24" id="mkin-09-24-2013-11-06">mkin 0.9-24 (2013-11-06)<a class="anchor" aria-label="anchor" href="#mkin-09-24-2013-11-06"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-24" id="mkin-09-24-2013-11-06">mkin 0.9-24 (2013-11-06)<a class="anchor" aria-label="anchor" href="#mkin-09-24-2013-11-06"></a></h2> <ul><li><p>Bugfix re-enabling the fixing of any combination of initial values for state variables</p></li> <li><p>Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions</p></li> <li><p>Backtransform fixed ODE parameters for the summary</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-22" id="mkin-09-22-2013-10-26">mkin 0.9-22 (2013-10-26)<a class="anchor" aria-label="anchor" href="#mkin-09-22-2013-10-26"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-22" id="mkin-09-22-2013-10-26">mkin 0.9-22 (2013-10-26)<a class="anchor" aria-label="anchor" href="#mkin-09-22-2013-10-26"></a></h2> <ul><li><p>Get rid of the optimisation step in <code>mkinerrmin</code> - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally</p></li> <li><p>Fix <code>plot.mkinfit</code> as it passed graphical arguments like main to the solver</p></li> <li><p>Do not use <code>plot=TRUE</code> in <code><a href="../reference/mkinfit.html">mkinfit()</a></code> example</p></li> @@ -683,28 +648,22 @@ <li><p>Do not use 0 values at time zero for chi2 error level calculations. This is the way it is done in KinGUII and it makes sense. It does impact the chi2 error levels in the output. Generally they seem to be lower for metabolites now, presumably because the mean of the observed values is higher</p></li> </ul><p>For a detailed list of changes to the mkin source please consult the commit history on <a href="http://github.com/jranke/mkin" class="external-link uri">http://github.com/jranke/mkin</a></p> </div> - </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> - - - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> |